[gmx-users] extracting coordinates from traj.xtc

mah maz mahmaz71 at gmail.com
Sun Dec 6 08:56:48 CET 2015

And also, if I want velocities for every step what can I do?

On Sun, Dec 6, 2015 at 11:19 AM, mah maz <mahmaz71 at gmail.com> wrote:

> Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr
> and traj.xtc. You are right both have the same data. I just need the
> coordinates to be readable a printable in a file now. Although I can write
> a program to extract the coordinates from gmxdump the way I need, it
> seems a bit time consuming. And I couldn't find a way yet! Is there a
> command like g_traj -f traj.trr -ox to print coordinates from traj.xtc?
> Thanks!
> On Thu, Dec 3, 2015 at 8:27 PM, mah maz <mahmaz71 at gmail.com> wrote:
>> Thanks Justin! I checked the run and it seemed ok. The fact is, the data
>> I get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout
>> it was set every 100 step by default), while the same command with g_traj
>> -f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every
>> step I need to extract them from traj.xtc. Can you suggest any ways?
>> Thank you!
>> On Tue, Dec 1, 2015 at 4:51 PM, mah maz <mahmaz71 at gmail.com> wrote:
>>> Thank you Justin. I expected that only water molecules are written in
>>> .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers
>>> like 1.64e-318 for all frames! How can I get real coordinates from .xtc?
>>> Thanks!
>>> On Tue, Dec 1, 2015 at 10:34 AM, mah maz <mahmaz71 at gmail.com> wrote:
>>>> Dear all,
>>>> I have some problems extracting data from traj.xtc. The command " g_
>>>> traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv"
>>>> but again couldn't get any results.  Note that I have nstxtcout = 1
>>>> and xtc_grps = water in my .mdp file.
>>>> Any help is appreciated.
>>>> Thank you!

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